Justin Silverman

Contact [email protected] justin-silverman.com Information statsathome.com

Research Bayesian statistics, time series analysis, multivariate analysis, sequence count data, Interests (e.g., microbiome surveys, gene expression studies, single cell RNA-seq), epidemiology, compositional data analysis, decision theory.

Employment Pennsylvania State University 2020- Assistant Professor, College of Information Science and Technology (Primary) Assistant Professor, Department of Medicine (Secondary)

Education MD and PhD, Duke University 2012-2020 PhD in Computational Biology and Bioinformatics Thesis: Bayesian Multivariate Count Models for the Design and Analysis of Microbiome Studies Mentors: Dr. Lawrence David and Dr. Sayan Mukherjee

Research Technician, Johns Hopkins University 2011-2012 Mentor: Dr. Nina Markovic

Bachelors of Science, Johns Hopkins University 2007-2011 Double Major in Physics and Biophysics, Minor in Mathematics

Publications [∗ denotes equal contribution]

Silverman JD∗, Hupert N, Washburne AD∗. Using influenza surveillance networks to estimate state-specific case detection-rates and forecast SARS-CoV-2 spread in the United States. (2020) medRxiv, DOI: 10.1101/2020.04.01.20050542

Morton J∗, Marotz C∗, Washburne A, Silverman JD, Edlund A, Zaramela L, Zengler K, Knight R. (2019) Establishing microbial measurement standards with reference frames. Nature Communications, 2719; DOI: 0.1038/s41467-019-10656-5

Villa MM∗, Bloom RJ∗, Silverman JD, Durand HK, Jiang S, Wu A, Huang S, You L, David LA. (2019) High-throughput isolation and culture of human gut bacteria with droplet microfluidics. bioRxiv 630822; DOI:10.1101/630822

Silverman JD, Bloom RJ, Jiang S, Durand HK, Mukherjee S, David LA. (2019) Mea- suring and Mitigating PCR Bias in Microbiome Data. bioRxiv 604025; DOI:10.1101/604025

Silverman JD, Roche K, Holmes ZC, David LA, Mukherjee S. (2019) Bayesian Multi- nomial Logistic Normal Models Through Marginally Latent Matrix-T Processes. arXiv :1903.11695

Silverman JD, Roche K, Mukherjee S, David LA. (2018) Naught all zeros in sequence count data are the same. bioRxiv 477794; DOI:10.1101/477794.

Silverman JD∗, Shenhav L∗, David LA, Halperin E, Mukherjee S. (2018) Statistical Considerations in the Design and Analysis of Longitudinal Microbiome Studies. bioRxiv 448332; DOI:10.1101/448332 (Invited Review at mSystems)

Curriculum Vitae, Justin Silverman, 1 Silverman JD, Durand HK, Bloom RJ, Mukherjee S, David LA. (2018) Dynamic linear models guide design and analysis of microbiota studies within artificial human guts. Microbiome. 6:202 DOI:10.1186/s40168-018-0584-3

Shenhav L, Furman O, Bariscoe L, Thompson M, Silverman JD, Mizrahi I, Halperin E. (2018) Modeling the temporal dynamics of the gut microbial community in adults and infants. bioRxiv 212993. DOI:10.1101/212993. (Submitted to PLoS Computational Biology)

Washburne AD, Silverman JD, Morton JT, Becker D, Crowley D, Mukherjee S, David LA, Plowright R. (2018) Phylofactorization - a graph partitioning algorithm to identify phylogenetic scales of ecological data. Ecological Monographs 00(00):e01353. DOI:10.1002/ecm.1353

Silverman JD, Silverman RK. (2018) The Bayesian Sorting Hat: A Decision-Theoretic Approach to Size-Constrained Clustering. arXiv:1710.06047. (In Revision at Journal of Machine Learning Research)

Midani FS, Weil AA, Chowdhury F, Begum YA, Khan AI, Debela, MD, Durand HK, Reese AT, Nimmagadda SN, Silverman JD, Ellis CN, Ryan ET, Calderwood SB, Harris JB, Qadri F, David LA, LaRocque RC. (2018) Human gut microbiota predicts susceptibility to Vibrio cholerae infection. The Journal of Infectious Diseases. 218:4 DOI:10.1093/infdis/jiy192

Silverman JD, Washburne AD, Mukherjee S, David LA. (2017) A phylogenetic transform enhances analysis of compositional microbiota data. eLife 6:e21887 DOI: 10.7554/eLife.21887

Washburne AD, Silverman JD, Leff JW, Bennett DJ, Darcy JL, Mukherjee S, Fierer N, David LA. (2017) Phylogenetic factorization of compositional data yields lineage- level associations in microbiome datasets. PeerJ 5:e2969 DOI:10.7717/peerj.2969

Patents and Justin D. Silverman (2019) Multinomial logistic-normal linear models using a marginal Software Laplace approximation (stray)

Justin D. Silverman (2019) R/C++ Header Library for Solving Minimum Cost Bipartite Matching Problems (RcppHungarian). R package Version 0.1. https://cran.r- project.org/web/packages/RcppHungarian/index.html

Justin D. Silverman (2019) R/C++ Header Library for Compositional Data Analysis (RcppCoDA)

Justin Silverman (2016) philr: Phylogenetic partitioning based ILR transform for metagenomics data. R package version 1.0.0. http://bioconductor.org/packages/philr/ (Downloaded 2951 times; September 6th, 2018).

Justin David Silverman, Adam Sean Jermyn, Nina Markovic. (2015) System for Lightweight Image Processing. U.S. Patent 9,097,739.

Curriculum Vitae, Justin Silverman, 2 Funded Research Duke Institute for Health Innovation, Innovation Award 2020-2021 “A Unified Framework for Predicting Bacteremia and Interpreting Blood Culture Results”

Collaborative Quantitative Approaches to Problems in Basic 2016-2017 and Clinical Sciences Authored (Submitting PIs: Lawrence David and Sayan Mukherjee) “A geometric approach to modeling human microbiota dynamics”

Honors and Best Young Presentation (Compositional Data Analysis Workshop) 2017 Awards Mitchell Meritorious Research Travel Award 2017 Phi Beta Kappa (JHU Highest Honors for Arts and Sciences) 2011 Donald E. Kerr Memorial Award for Excellence in Physics 2011 H. Keffer Hartline Award for Outstanding Scholarship in Biophysics 2011 JHU Office of Greek Life Senior Academic Excellence Award 2011 Goldwater Scholar 2010 Provost Undergraduate Research Award 2010 Materials Research Science and Engineering Center, Summer REU 2010 Sigma Pi Sigma (Physics Honor Society, Invitation Only) 2010

Service Referee publons.com/author/1257294/justin-d-silverman Annals of Applied Statistics PLoS Genetics PLoS Computational Biology mSystems Microbiome SORT NAR Genomics and Bioinformatics Session Organizer IMS Invited Session at JSM 2018 “Longitudinal Modeling and Experimental Design for Investigating Host Associated Microbiota”

Invited Talks ENAR Compositional Nature of Microbiome Data: Challenges and New Methods 2020 Symposium on Advances in Genomics, Epidemiology and Statistics: Philadelphia 2019 Biostatistics Seminar Series at University of Massachusetts: Amherst, MA 2019 Simons Foundation: New York, NY 2019 Penn State University: State College, PA 2019 University of Chicago: Chicago, IL 2019 Computational Molecular Biology Seminar at Brown: Providence, RI 2018 Center of Statistical Genetics Seminar, Univ of Michigan: Ann Arbor, MI 2018 IMS Invited Session at JSM: Vancouver, BC 2018 Probabilistic Microbial Modeling Symposium: San Diego, CA 2018 ENAR Geometry and Topology in Statistical Inference: Atlanta, GA 2018 Wharton Statistics Seminar Series: Philadelphia, PA 2018 Universitat Polit`ecnicade Catalunya: Barcelona, Spain 2018 Seminar in Compositional Data: Girona, Spain 2017 Health Analytics Workshop at Duke University: Durham, NC 2016

Conference Modeling time evolution and therapeutic effect in human microbiota, The 7th Interna- Talks tional Workshop on Compositional Data Analysis, Abbadia San Salvatore, Italy. (June 2017)

Curriculum Vitae, Justin Silverman, 3 Research Kim Roche (Graduate) 2018-2019 Mentorship Katie Sparks (Undergraduate) 2012 Chris Weddel (High School) 2011-2012 Adam Jermyn (High School) 2011-2012 Roberto Rivera (Undergraduate) 2011

Teaching DOmath 2018 Research Program: Summer 2018 Experience Stochastic Properties of Dynamical Systems: Project Manager

Human Microbiome Seminar Spring 2017 Guest Lecturer, University of North Carolina, Chapel Hill

Statistical Methods in Computational Biology Spring 2017 Teaching Assistant and Guest Lecturer, Duke University

Spectroscopy (Quantum Mechanics for Biophysics) Fall 2011 Teaching Assistant, Johns Hopkins University

References Sayan Mukherjee, Professor, Department of Statistical Science, Duke University, (919) 684-4608 [email protected]

Lawrence David, Assistant Professor, Center for Genomic and Computational Bi- ology, Duke University, (919) 668-5388 [email protected]

Juan Jose Egozcue, Professor, Department of Civil and Environmental Engineer- ing, Polytechnic University of Catelonia, [email protected]

Vera Pawlowsky-Glahn, Professor, Department of Computer Science and Applied Math, University of Girona, ++34-972-418170, [email protected]

Greg Gloor, Professor, Department of Biochemistry, University of Western Ontario, (519) 661-2111, [email protected]

David Simel, Professor, Department of Medicine, Duke University, (919) 286-6941, [email protected]

Curriculum Vitae, Justin Silverman, 4